Degenerate oligonucleotide primed-polymerase chain reaction-based array comparative genomic hybridization for extensive amplicon profiling of breast cancers - A new approach for the molecular analysis of paraffin-embedded cancer tissue

We have developed a protocol for degenerate oligonuclotide-primed-polymeras e chain reaction-based array comparative genomic hybridization (array CGH) that, when combined with a laser microdissection technique, allows the anal ysis of cancer cell populations isolated from routine, formalin-axed, paraf fin-embedded tissue samples. Comparison of copy number changes detected by degenerate oligonucleotide-primed-polymerase chain reaction-based array CGH to those detected by conventional array CGH or fluorescence ill situ hybri dization, demonstrated that amplifications can be reliably detected. Using a genomic microarray containing 57 oncogenes, we screened a total of 28 bre ast cancer samples and obtained a detailed amplicon profile that is the mos t comprehensive to date in human breast cancer. The array CGH method descri bed here will allow the genetic analysis of paraffin-embedded human cancer materials for example in the context of clinical trials.